Data

This data was taken from a clean dataset that Jae emailed out on November 26th, 2019.

Jae organized the retina by six different methods. He created OCTA variable scores for the overall image, 2 hemifields, 4 quadrants, 6 sectors, 12 clock hours, and an annular ring.

Annular image scoring was also assessed, and ICC’s were similar, but slightly lower than global. Results for annular image scoring are not shown. For now, only the overall “global” image scoring will be shown.

Zeiss commercial vessel area density and flux variables are also shown for the global image scoring.

Data Wrangling

Rename Variables

This section will rename the variables to match the dictionary

Label Variables

This section will label variables appropriately.

Data Dictionary

Variable Label
ptid Patient Identification
Sociodemographic Variables
age Age
female Sex
Systemic Clinical Variables
htn_dx Hypertension Diagnosis
dm_dx Diabetes Mellitus Diagnosis
nro_dx Optic Neuropathy
Ophthalmic Clinical Variables
dr_dx Diabetic Retinopathy Diagnosis, Ordinal
dr_dx_bin Diabetic Retinopathy Diagnosis, Binary
glc_sus_dx Glaucoma Suspect Diagnosis
glc_dx Glaucoma Diagnosis, Ordinal
glc_dx_bin Glaucoma Diagnosis, Binary
surg_proc_glaucoma Surgical Procedure for Glaucoma
OCT Angiography Variables
surg_proc_catextract Surgical Procedure for Cataract Extraction
eyeid Eye Identification
eye_imaged Eye Imaged
time_stamp Exam Date and Time
name_last Last Name
name_first First Name
image_area Image Area
image_method Image Method
image_size Image Size
signal_strength Signal Strength
v_diameter Vessel Diameter (units?)
v_area_density Vessel Area Density (units?)
v_skeleton_density Vessel Skeleton Density (units?)
v_perimeter_index Vessel Perimeter Index (units?)
v_complexity_index Vessel Complexity Index (units?)
flow_impair_zone Flow Impairment Zone (units?)
flux Flux (units?)
zeiss_v_area_density Vessel Area Density (units?), Zeiss Commercial
zeiss_flux Flux (units?), Zeiss Commercial

Single Eye Participation

Venugopal (2019) et al. ran the analysis including all eyes.1 Then they re-ran the analysis after selecting only a single eye randomly from each individual. They conclude minimal difference in the findings, and they report only the analysis that includes all eyes:

“The entire analysis was repeated considering one eye per subject (one eye was randomly chosen from subjects contributing both eyes for the primary analysis) and all the results were similar to the primary analysis.”1

The following results are for the single eye, chosen at random, from each participant. Bruce did explain a way to calculate ICC’s for all measurements on both eyes of each participant. This will be coded later.

Subsetting Cohorts

Intra-Visit Data

Intra-visit data was restricted to all measurements of the same eye that occurred on the same day. Some people had multiple measurements on multiple days. Their first day was included only.

Inter-Visit Data

Inter-visit data was restricted to the first measurement of the day for each eye. If a patient had their right eye measured:

  • 3 times on Monday

  • 5 times on Wednesday, and

  • 2 times on Friday,

Then they would have three observations in this dataset:

  • The first measurement from Monday,

  • The first measurement from Wednesday, and

  • The first measurement from Friday.

Data Flow Chart

This tallies how many participants, how many eyes, and how many measurements are included in the two datasets.

dataset n_participants n_eyes n_measurements
Global Data
Intra-Visit 149 149 386
Inter-Visit 148 148 386

Overall there were:

  • 332 measurements of 68 patients without glaucoma

  • 462 measurements of 81 patients with glaucoma

Among intravisit data there were:

  • 180 measurements of 68 patients without glaucoma

  • 206 measurements of 81 patients with glaucoma

Among intervisit data there were:

  • 151 measurements of 67 patients without glaucoma

  • 235 measurements of 81 patients with glaucoma

Table 1: Summary Statistics

Note to Dom: Something weird is occuring with Table 1…need to debug because it shows 82 glaucoma patients, but we’re saying only 81 when looking directly at the data (above).

Intra-Visit OCTA Summary Statistics

Variables in intra-visit dataset

Participants

None Glaucoma p test
n 68 82
Sociodemographic Variables
age (mean (SD)) 50.74 (16.26) 61.78 (14.50) <0.001
Sex = Male (%) 33 (48.5) 39 ( 47.6) 1.000
Systemic Clinical Variables
Hypertension Diagnosis = Yes (%) 15 (22.1) 28 ( 34.1) 0.148
Diabetes Mellitus Diagnosis = Yes (%) 3 ( 4.4) 14 ( 17.1) 0.030
Optic Neuropathy = Yes (%) 1 ( 1.5) 0 ( 0.0) 0.925
Ophthalmic Clinical Variables
Glaucoma Diagnosis, Binary = Glaucoma (%) 0 ( 0.0) 82 (100.0) <0.001
Diabetic Retinopathy Diagnosis, Binary = Yes (%) 0 ( 0.0) 4 ( 4.9) 0.181
Ophthalmic Surgical Variables
Surgical Procedure for Cataract Extraction = Yes (%) 8 (11.8) 21 ( 25.6) 0.054
Surgical Procedure for Glaucoma (%) <0.001
None 62 (91.2) 45 ( 54.9)
Laser 6 ( 8.8) 18 ( 22.0)
Minimally Invasive Glaucoma Surgery 0 ( 0.0) 1 ( 1.2)
Filter 0 ( 0.0) 18 ( 22.0)
OCT Angiography Signal Strength
signal_strength (mean (SD)) 9.50 (0.64) 9.16 (0.79) 0.005

Measurements

Normal Glaucoma p test
n 180 206
Sociodemographic Variables
age (mean (SD)) 50.18 (16.53) 60.82 (15.03) <0.001
Sex = Male (%) 88 ( 48.9) 96 ( 46.6) 0.729
Systemic Clinical Variables
Hypertension Diagnosis = Yes (%) 40 ( 22.2) 67 ( 32.5) 0.032
Diabetes Mellitus Diagnosis = Yes (%) 6 ( 3.3) 33 ( 16.0) <0.001
Optic Neuropathy = Yes (%) 3 ( 1.7) 0 ( 0.0) 0.201
Diabetic Retinopathy Diagnosis
Diabetic Retinopathy Diagnosis, Ordinal (%) NaN
None 180 (100.0) 197 ( 95.6)
Mild Non-Proliferative Diabetic Retinopathy 0 ( 0.0) 5 ( 2.4)
Moderate Non-Proliferative Diabetic Retinopathy 0 ( 0.0) 2 ( 1.0)
Severe Non-Proliferative Diabetic Retinopathy 0 ( 0.0) 2 ( 1.0)
Proliferative Diabetic Retinopathy 0 ( 0.0) 0 ( 0.0)
Glaucoma Suspect Diagnosis
Glaucoma Suspect Diagnosis (%) <0.001
None 5 ( 2.8) 206 (100.0)
Mild 90 ( 50.0) 0 ( 0.0)
Moderate 47 ( 26.1) 0 ( 0.0)
Severe 38 ( 21.1) 0 ( 0.0)
Glaucoma Diagnosis, Ordinal
Glaucoma Diagnosis, Ordinal (%) <0.001
None 180 (100.0) 0 ( 0.0)
Mild 0 ( 0.0) 78 ( 37.9)
Moderate 0 ( 0.0) 60 ( 29.1)
Severe 0 ( 0.0) 68 ( 33.0)
Surgical Procedure for Glaucoma
Surgical Procedure for Glaucoma (%) <0.001
None 164 ( 91.1) 119 ( 57.8)
Laser 16 ( 8.9) 43 ( 20.9)
Minimally Invasive Glaucoma Surgery 0 ( 0.0) 3 ( 1.5)
Filter 0 ( 0.0) 41 ( 19.9)
Surgical Procedure for Cataract Extraction
Surgical Procedure for Cataract Extraction = Yes (%) 20 ( 11.1) 49 ( 23.8) 0.002
Image Specifications
Eye Imaged = Right (%) 96 ( 53.3) 83 ( 40.3) 0.014
Image Area = ONH5 (%) 0 ( 0.0) 4 ( 1.9) 0.169
Image Method = Angiography (%) 180 (100.0) 206 (100.0) NA
Image Size = 6x6 (%) 180 (100.0) 206 (100.0) NA
OCT Angiography Signal Strength
Signal Strength (%) 0.004
7 2 ( 1.1) 7 ( 3.4)
8 18 ( 10.0) 40 ( 19.4)
9 46 ( 25.6) 62 ( 30.1)
10 114 ( 63.3) 97 ( 47.1)
OCT Angiography Variables
v_diameter (mean (SD)) 25.89 (0.74) 27.23 (1.60) <0.001
v_area_density (mean (SD)) 0.36 (0.04) 0.28 (0.07) <0.001
zeiss_v_area_density (mean (SD)) 0.43 (0.02) 0.40 (0.04) <0.001
v_skeleton_density (mean (SD)) 0.14 (0.02) 0.10 (0.03) <0.001
v_perimeter_index (mean (SD)) 0.31 (0.04) 0.24 (0.06) <0.001
v_complexity_index (mean (SD)) 7830.72 (961.58) 6018.03 (1576.13) <0.001
flow_impair_zone (mean (SD)) 9.82 (3.48) 15.94 (5.51) <0.001
flux (mean (SD)) 0.11 (0.02) 0.08 (0.03) <0.001
zeiss_flux (mean (SD)) 0.36 (0.02) 0.32 (0.04) <0.001

Inter-Visit OCTA Summary Statistics

Variables in inter-visit dataset

Participants

None Glaucoma p test
n 67 82
Sociodemographic Variables
age (mean (SD)) 51.13 (16.04) 61.78 (14.50) <0.001
Sex = Male (%) 32 (47.8) 39 ( 47.6) 1.000
Systemic Clinical Variables
Hypertension Diagnosis = Yes (%) 15 (22.4) 28 ( 34.1) 0.163
Diabetes Mellitus Diagnosis = Yes (%) 3 ( 4.5) 14 ( 17.1) 0.032
Optic Neuropathy = Yes (%) 1 ( 1.5) 0 ( 0.0) 0.919
Ophthalmic Clinical Variables
Glaucoma Diagnosis, Binary = Glaucoma (%) 0 ( 0.0) 82 (100.0) <0.001
Diabetic Retinopathy Diagnosis, Binary = Yes (%) 0 ( 0.0) 4 ( 4.9) 0.186
Ophthalmic Surgical Variables
Surgical Procedure for Cataract Extraction = Yes (%) 8 (11.9) 21 ( 25.6) 0.059
Surgical Procedure for Glaucoma (%) <0.001
None 61 (91.0) 45 ( 54.9)
Laser 6 ( 9.0) 18 ( 22.0)
Minimally Invasive Glaucoma Surgery 0 ( 0.0) 1 ( 1.2)
Filter 0 ( 0.0) 18 ( 22.0)
OCT Angiography Signal Strength
signal_strength (mean (SD)) 9.45 (0.66) 9.13 (0.70) 0.005

Measurements

Normal Glaucoma p test
n 151 235
Sociodemographic Variables
age (mean (SD)) 51.46 (15.98) 58.79 (16.32) <0.001
Sex = Male (%) 71 ( 47.0) 109 ( 46.4) 0.986
Systemic Clinical Variables
Hypertension Diagnosis = Yes (%) 35 ( 23.2) 76 ( 32.3) 0.068
Diabetes Mellitus Diagnosis = Yes (%) 6 ( 4.0) 37 ( 15.7) 0.001
Optic Neuropathy = Yes (%) 3 ( 2.0) 0 ( 0.0) 0.115
Diabetic Retinopathy Diagnosis
Diabetic Retinopathy Diagnosis, Ordinal (%) NaN
None 151 (100.0) 225 ( 95.7)
Mild Non-Proliferative Diabetic Retinopathy 0 ( 0.0) 6 ( 2.6)
Moderate Non-Proliferative Diabetic Retinopathy 0 ( 0.0) 2 ( 0.9)
Severe Non-Proliferative Diabetic Retinopathy 0 ( 0.0) 2 ( 0.9)
Proliferative Diabetic Retinopathy 0 ( 0.0) 0 ( 0.0)
Glaucoma Suspect Diagnosis
Glaucoma Suspect Diagnosis (%) <0.001
None 5 ( 3.3) 235 (100.0)
Mild 69 ( 45.7) 0 ( 0.0)
Moderate 40 ( 26.5) 0 ( 0.0)
Severe 37 ( 24.5) 0 ( 0.0)
Glaucoma Diagnosis, Ordinal
Glaucoma Diagnosis, Ordinal (%) <0.001
None 151 (100.0) 0 ( 0.0)
Mild 0 ( 0.0) 89 ( 37.9)
Moderate 0 ( 0.0) 63 ( 26.8)
Severe 0 ( 0.0) 83 ( 35.3)
Surgical Procedure for Glaucoma
Surgical Procedure for Glaucoma (%) <0.001
None 138 ( 91.4) 131 ( 55.7)
Laser 13 ( 8.6) 44 ( 18.7)
Minimally Invasive Glaucoma Surgery 0 ( 0.0) 2 ( 0.9)
Filter 0 ( 0.0) 58 ( 24.7)
Surgical Procedure for Cataract Extraction
Surgical Procedure for Cataract Extraction = Yes (%) 20 ( 13.2) 53 ( 22.6) 0.032
Image Specifications
Eye Imaged = Right (%) 75 ( 49.7) 105 ( 44.7) 0.393
Image Area = ONH5 (%) 0 ( 0.0) 8 ( 3.4) 0.054
Image Method = Angiography (%) 151 (100.0) 235 (100.0) NA
Image Size = 6x6 (%) 151 (100.0) 235 (100.0) NA
OCT Angiography Signal Strength
Signal Strength (%) 0.009
7 5 ( 3.3) 10 ( 4.3)
8 17 ( 11.3) 45 ( 19.1)
9 38 ( 25.2) 79 ( 33.6)
10 91 ( 60.3) 101 ( 43.0)
OCT Angiography Variables
v_diameter (mean (SD)) 25.85 (0.81) 27.35 (1.72) <0.001
v_area_density (mean (SD)) 0.36 (0.05) 0.28 (0.07) <0.001
zeiss_v_area_density (mean (SD)) 0.43 (0.02) 0.39 (0.04) <0.001
v_skeleton_density (mean (SD)) 0.14 (0.02) 0.10 (0.03) <0.001
v_perimeter_index (mean (SD)) 0.31 (0.04) 0.24 (0.06) <0.001
v_complexity_index (mean (SD)) 7795.79 (1093.84) 5951.39 (1624.45) <0.001
flow_impair_zone (mean (SD)) 9.92 (4.02) 16.14 (5.67) <0.001
flux (mean (SD)) 0.11 (0.02) 0.08 (0.03) <0.001
zeiss_flux (mean (SD)) 0.36 (0.03) 0.32 (0.03) <0.001

Exploratory Data Analysis

Scatter Plots

Scatter plots of OCTA variables by Subject ID for about 10 individuals randomly sampled. These are separated by intra- and inter-visit datasets, and are useful for understanding the data better.

Vessel Area Density

Vessel Area Density, Zeiss

Vessel Diameter

Vessel Skeleton Density

Vessel Perimeter Index

Vessel Complexity Index

Flow Impairment Zone

Flux

Flux, Zeiss

Spaghetti Plots

Spaghetti plots of OCTA variables for about 10 individuals randomly sampled.

Vessel Area Density

Vessel Area Density, Zeiss

Vessel Diameter

Vessel Skeleton Density

Vessel Perimeter Index

Vessel Complexity Index

Flow Impairment Zone

Flux

Flux, Zeiss

Bland-Altman Plots

Coding of Bland-Altman (BA) plots is explained in this blog post.

Intra-Visit Bland-Altman Plots

Intra-Visit Bland-Altman Plots of OCTA Variables

Vessel Area Density

Vessel Area Density, Zeiss

Vessel Diameter

Vessel Skeleton Density

Vessel Perimeter Index

Vessel Complexity Index

Flow Impairment Zone

Flux

Flux, Zeiss

Outliers

Assess some of the observations outside of expected limits.

eyeid ptid signal_strength female eye_imaged image_area image_size image_method exam_date time_stamp v_diameter v_area_density v_skeleton_density v_perimeter_index v_complexity_index flow_impair_zone flux zeiss_v_area_density zeiss_flux age htn_dx dm_dx nro_dx dr_dx glc_sus_dx glc_dx surg_proc_glaucoma surg_proc_catextract glc_dx_bin dr_dx_bin n_msr_day order_obs
42 1787031 9 Female Right ONH 6x6 Angiography 2019-04-10 2019-04-10 11:47:25 26.79852 0.2269611 0.08469167 0.1965333 4875.438 19.4988 0.06092570 0.386 0.286 52.0 No No No None Severe None None Yes Normal No 2 1
42 1787031 8 Female Right ONH 6x6 Angiography 2019-04-10 2019-04-10 11:47:52 26.37865 0.3541333 0.13425000 0.3041139 7481.666 10.8069 0.10075818 0.378 0.280 52.0 No No No None Severe None None Yes Normal No 2 2
183 7281737 9 Female Left ONH 6x6 Angiography 2019-02-08 2019-02-08 09:40:28 27.39412 0.2704028 0.09870833 0.2328444 5743.984 15.3945 0.06712986 0.380 0.301 72.3 No No No None None Moderate None Yes Glaucoma No 3 1
183 7281737 8 Female Left ONH 6x6 Angiography 2019-02-08 2019-02-08 09:40:59 26.34979 0.3205306 0.12164444 0.2765944 6837.701 9.8990 0.08433553 0.371 0.298 72.3 No No No None None Moderate None Yes Glaucoma No 3 2
183 7281737 9 Female Left ONH 6x6 Angiography 2019-02-08 2019-02-08 09:41:30 26.20672 0.3136944 0.11970000 0.2727444 6793.563 12.4437 0.08991662 0.403 0.320 72.3 No No No None None Moderate None Yes Glaucoma No 3 3
208 7519765 8 Male Left ONH 6x6 Angiography 2019-08-30 2019-08-30 15:30:14 28.61262 0.2290361 0.08004722 0.1944417 4728.979 20.7554 0.05636949 0.367 0.295 61.0 Yes No No None None Severe Laser Yes Glaucoma No 2 1
208 7519765 10 Male Left ONH 6x6 Angiography 2019-08-30 2019-08-30 15:32:55 27.09403 0.2790083 0.10297778 0.2371056 5772.433 15.6147 0.07661490 0.379 0.328 61.0 Yes No No None None Severe Laser Yes Glaucoma No 2 2
220 7618939 9 Male Right ONH 6x6 Angiography 2019-11-01 2019-11-01 10:00:51 25.03574 0.3570444 0.14261389 0.3129611 7858.707 8.1060 0.10365880 0.425 0.358 63.9 No No No None Mild None None Yes Normal No 2 1
220 7618939 9 Male Right ONH 6x6 Angiography 2019-11-01 2019-11-01 10:01:46 30.30372 0.1674028 0.05524167 0.1359583 3163.309 25.8999 0.03618447 0.416 0.344 63.9 No No No None Mild None None Yes Normal No 2 2
239 7774801 7 Male Left ONH 6x6 Angiography 2019-09-04 2019-09-04 11:18:39 27.31514 0.2397056 0.08775556 0.2072472 5133.245 18.0851 0.06471167 0.393 0.294 48.0 No No No None None Severe Laser No Glaucoma No 3 1
239 7774801 8 Male Left ONH 6x6 Angiography 2019-09-04 2019-09-04 11:19:17 27.36307 0.2252361 0.08231389 0.1964972 4910.972 24.2861 0.05995696 0.386 0.288 48.0 No No No None None Severe Laser No Glaucoma No 3 2
239 7774801 7 Male Left ONH 6x6 Angiography 2019-09-04 2019-09-04 11:20:04 27.46280 0.2363556 0.08606389 0.2067306 5180.076 18.6636 0.06396713 0.396 0.297 48.0 No No No None None Severe Laser No Glaucoma No 3 3

Inter-Visit Bland-Altman Plots

Inter-Visit Bland-Altman Plots of OCTA Variables

Vessel Area Density

Vessel Area Density, Zeiss

Vessel Diameter

Vessel Skeleton Density

Vessel Perimeter Index

Vessel Complexity Index

Flow Impairment Zone

Flux

Flux, Zeiss

Outliers

Assess some of the observations outside of expected limits.

eyeid ptid signal_strength female eye_imaged image_area image_size image_method exam_date time_stamp v_diameter v_area_density v_skeleton_density v_perimeter_index v_complexity_index flow_impair_zone flux zeiss_v_area_density zeiss_flux age htn_dx dm_dx nro_dx dr_dx glc_sus_dx glc_dx surg_proc_glaucoma surg_proc_catextract glc_dx_bin dr_dx_bin order_obs day_one diff_date ind_n_day n_exams
42 1787031 8 Female Right ONH 6x6 Angiography 2018-10-10 2018-10-10 10:45:55 26.00271 0.3302417 0.12700278 0.2890167 7246.137 12.2366 0.09268497 0.380 0.288 52.0 No No No None Severe None None Yes Normal No 1 2018-10-10 0 days 1 3
42 1787031 9 Female Right ONH 6x6 Angiography 2019-04-10 2019-04-10 11:47:25 26.79852 0.2269611 0.08469167 0.1965333 4875.438 19.4988 0.06092570 0.386 0.286 52.0 No No No None Severe None None Yes Normal No 2 2018-10-10 182 days 1 3
42 1787031 7 Female Right ONH 6x6 Angiography 2019-05-08 2019-05-08 11:09:31 26.18709 0.3000750 0.11458889 0.2632389 6615.504 14.1551 0.08483724 0.380 0.278 52.0 No No No None Severe None None Yes Normal No 3 2018-10-10 210 days 1 3
75 2360743 10 Male Left ONH 6x6 Angiography 2018-08-27 2018-08-27 16:11:17 27.62141 0.2892806 0.10473056 0.2462556 6005.449 16.0287 0.08665999 0.291 0.306 63.0 No No No None None Moderate None No Glaucoma No 1 2018-08-27 0 days 1 6
75 2360743 10 Male Left ONH 6x6 Angiography 2019-03-04 2019-03-04 17:12:06 32.10996 0.1438972 0.04481389 0.1236000 3041.425 26.1068 0.03381287 0.302 0.308 63.0 No No No None None Moderate None No Glaucoma No 2 2018-08-27 189 days 1 6
75 2360743 9 Male Left ONH 6x6 Angiography 2019-07-19 2019-07-19 11:00:41 28.58143 0.2540333 0.08888056 0.2073083 4846.581 18.1739 0.06822889 0.297 0.292 63.0 No No No None None Moderate None No Glaucoma No 3 2018-08-27 326 days 1 6
75 2360743 9 Male Left ONH 6x6 Angiography 2019-09-13 2019-09-13 10:16:26 28.13602 0.2571944 0.09141111 0.2124639 5028.070 17.9982 0.06763857 0.293 0.289 63.0 No No No None None Moderate None No Glaucoma No 4 2018-08-27 382 days 1 6
75 2360743 10 Male Left ONH 6x6 Angiography 2019-10-18 2019-10-18 10:00:02 27.68875 0.2463222 0.08896111 0.2049611 4885.758 19.0984 0.06262440 0.304 0.288 63.0 No No No None None Moderate None No Glaucoma No 5 2018-08-27 417 days 1 6
75 2360743 9 Male Left ONH 6x6 Angiography 2019-11-22 2019-11-22 09:52:43 28.34473 0.2522444 0.08899167 0.2082472 4925.263 18.1297 0.06423940 0.299 0.299 63.0 No No No None None Moderate None No Glaucoma No 6 2018-08-27 452 days 1 6
82 35357 10 Female Left ONH 6x6 Angiography 2017-03-16 2017-03-16 15:01:12 25.89829 0.2428972 0.09378889 0.2142194 5412.375 18.7766 0.06262892 0.438 0.331 80.0 No No No None None Mild None Yes Glaucoma No 1 2017-03-16 0 days 1 2
82 35357 10 Female Left ONH 6x6 Angiography 2019-11-06 2019-11-06 09:13:11 24.70524 0.3272278 0.13245278 0.2905139 7388.840 10.8254 0.09269607 0.446 0.338 80.0 No No No None None Mild None Yes Glaucoma No 2 2017-03-16 965 days 1 2
92 51313 8 Female Right ONH 6x6 Angiography 2019-05-03 2019-05-03 14:18:00 27.52564 0.2005778 0.07286944 0.1777028 4510.225 23.5351 0.05143312 0.393 0.262 65.4 No No No None None Severe None No Glaucoma No 1 2019-05-03 0 days 1 2
92 51313 10 Female Right ONH 6x6 Angiography 2019-10-04 2019-10-04 13:46:37 26.29430 0.2731028 0.10386389 0.2406278 6073.766 14.0610 0.07163423 0.377 0.296 65.4 No No No None None Severe None No Glaucoma No 2 2019-05-03 154 days 1 2
220 7618939 8 Male Right ONH 6x6 Angiography 2019-09-27 2019-09-27 09:31:48 30.44544 0.1959333 0.06435556 0.1615389 3815.386 23.2141 0.04367739 0.421 0.330 63.9 No No No None Mild None None Yes Normal No 1 2019-09-27 0 days 1 2
220 7618939 9 Male Right ONH 6x6 Angiography 2019-11-01 2019-11-01 10:00:51 25.03574 0.3570444 0.14261389 0.3129611 7858.707 8.1060 0.10365880 0.425 0.358 63.9 No No No None Mild None None Yes Normal No 2 2019-09-27 35 days 1 2
232 7685911 10 Male Left ONH 6x6 Angiography 2019-05-17 2019-05-17 09:36:40 25.26540 0.3918944 0.15511111 0.3452444 8713.185 7.2402 0.12386042 0.456 0.377 41.9 No No No None Mild None None No Normal No 1 2019-05-17 0 days 1 2
232 7685911 7 Male Left ONH 6x6 Angiography 2019-10-25 2019-10-25 09:03:28 25.67694 0.2875389 0.11198333 0.2564194 6550.855 15.7090 0.08239656 0.438 0.328 41.9 No No No None Mild None None No Normal No 2 2019-05-17 161 days 1 2

Repeatability

Repeatability of OCTA Variables

Calculate the within-subject standard deviation \((S_w)\), the within-subject coefficient of repeatability \((CR_w)\), and the within-subject coefficient of variation \((CV_w)\) for a given measurement variable \(x\).

Table 2: Repeatability

Table 2 shows repeatability estimates of vessel density measurements.

This table was modeled after Table 2 in Venugopal (2018).2

Intra-Visit Repeatability

Normal

OCTA Variable n_measure µ Sw Sw 95% CL CRw CRw 95% CL CVw CVw 95% CL
Vessel Diameter (units?) 180 25.891 0.461 (0.248, 0.674) 1.278 (0.689, 1.868) 1.781 (0.959, 2.603)
Vessel Area Density (units?) 180 0.359 0.021 (0.021, 0.021) 0.059 (0.058, 0.059) 5.884 (5.800, 5.967)
Vessel Area Density (units?), Zeiss Commercial 180 0.429 0.006 (0.006, 0.006) 0.016 (0.016, 0.016) 1.369 (1.368, 1.371)
Vessel Skeleton Density (units?) 180 0.139 0.009 (0.009, 0.009) 0.026 (0.026, 0.026) 6.716 (6.672, 6.760)
Vessel Perimeter Index (units?) 180 0.313 0.019 (0.019, 0.019) 0.053 (0.052, 0.053) 6.059 (5.977, 6.140)
Vessel Complexity Index (units?) 180 7830.721 489.263 (-175520.576, 176499.102) 1356.168 (-486518.216, 489230.552) 6.248 (-2241.436, 2253.932)
Flow Impairment Zone (units?) 180 9.819 1.925 (-0.560, 4.411) 5.337 (-1.553, 12.226) 19.608 (-5.705, 44.920)
Flux (units?) 180 0.108 0.008 (0.008, 0.008) 0.022 (0.022, 0.023) 7.485 (7.451, 7.520)
Flux (units?), Zeiss Commercial 180 0.360 0.007 (0.007, 0.007) 0.018 (0.018, 0.018) 1.847 (1.844, 1.849)

Glaucoma

OCTA Variable n_measure µ Sw Sw 95% CL CRw CRw 95% CL CVw CVw 95% CL
Vessel Diameter (units?) 206 27.226 0.474 (0.393, 0.556) 1.315 (1.089, 1.541) 1.743 (1.443, 2.042)
Vessel Area Density (units?) 206 0.281 0.019 (0.019, 0.019) 0.052 (0.051, 0.052) 6.642 (6.609, 6.674)
Vessel Area Density (units?), Zeiss Commercial 206 0.398 0.007 (0.007, 0.007) 0.019 (0.019, 0.019) 1.748 (1.746, 1.751)
Vessel Skeleton Density (units?) 206 0.105 0.008 (0.008, 0.008) 0.023 (0.022, 0.023) 7.751 (7.734, 7.767)
Vessel Perimeter Index (units?) 206 0.243 0.017 (0.017, 0.017) 0.047 (0.047, 0.047) 7.001 (6.969, 7.034)
Vessel Complexity Index (units?) 206 6018.028 443.845 (-55478.735, 56366.424) 1230.274 (-153779.209, 156239.757) 7.375 (-921.876, 936.626)
Flow Impairment Zone (units?) 206 15.939 1.829 (1.035, 2.624) 5.071 (2.868, 7.274) 11.477 (6.491, 16.463)
Flux (units?) 206 0.079 0.007 (0.007, 0.007) 0.019 (0.019, 0.019) 8.479 (8.465, 8.492)
Flux (units?), Zeiss Commercial 206 0.320 0.007 (0.007, 0.007) 0.019 (0.019, 0.019) 2.098 (2.095, 2.101)

Inter-Visit Repeatability

Restrict to repeat measurements within the last 6 months.

Normal, 180 Days

There are way too few measurements for this table to be reliable.

OCTA Variable n_measure µ Sw Sw 95% CL CRw CRw 95% CL CVw CVw 95% CL
Vessel Diameter (units?) 42 25.755 0.929 (-0.016, 1.873) 2.574 (-0.045, 5.193) 3.606 (-0.063, 7.274)
Vessel Area Density (units?) 42 0.362 0.035 (0.034, 0.036) 0.097 (0.095, 0.100) 9.694 (9.451, 9.936)
Vessel Area Density (units?), Zeiss Commercial 42 0.431 0.009 (0.009, 0.009) 0.024 (0.024, 0.024) 2.040 (2.034, 2.046)
Vessel Skeleton Density (units?) 42 0.141 0.016 (0.016, 0.016) 0.045 (0.044, 0.045) 11.479 (11.336, 11.621)
Vessel Perimeter Index (units?) 42 0.316 0.032 (0.031, 0.033) 0.088 (0.086, 0.090) 10.052 (9.812, 10.293)
Vessel Complexity Index (units?) 42 7908.515 824.478 (-534984.198, 536633.154) 2285.337 (-1482900.540, 1487471.214) 10.425 (-6764.660, 6785.511)
Flow Impairment Zone (units?) 42 9.180 3.205 (-4.350, 10.760) 8.884 (-12.058, 29.825) 34.911 (-47.386, 117.208)
Flux (units?) 42 0.107 0.014 (0.013, 0.014) 0.038 (0.037, 0.038) 12.648 (12.533, 12.763)
Flux (units?), Zeiss Commercial 42 0.357 0.014 (0.013, 0.014) 0.038 (0.037, 0.038) 3.790 (3.767, 3.812)

Glaucoma, 180 Days

OCTA Variable n_measure µ Sw Sw 95% CL CRw CRw 95% CL CVw CVw 95% CL
Vessel Diameter (units?) 119 27.750 0.490 (0.436, 0.544) 1.358 (1.207, 1.508) 1.765 (1.570, 1.960)
Vessel Area Density (units?) 119 0.260 0.023 (0.023, 0.023) 0.064 (0.063, 0.064) 8.829 (8.787, 8.872)
Vessel Area Density (units?), Zeiss Commercial 119 0.390 0.009 (0.009, 0.009) 0.026 (0.026, 0.026) 2.424 (2.419, 2.428)
Vessel Skeleton Density (units?) 119 0.096 0.009 (0.009, 0.009) 0.026 (0.026, 0.026) 9.775 (9.756, 9.794)
Vessel Perimeter Index (units?) 119 0.224 0.020 (0.020, 0.020) 0.057 (0.056, 0.057) 9.111 (9.071, 9.151)
Vessel Complexity Index (units?) 119 5529.773 520.899 (-58453.849, 59495.647) 1443.859 (-162025.802, 164913.521) 9.420 (-1057.075, 1075.915)
Flow Impairment Zone (units?) 119 17.636 2.620 (1.097, 4.142) 7.261 (3.040, 11.482) 14.854 (6.220, 23.488)
Flux (units?) 119 0.072 0.008 (0.008, 0.008) 0.023 (0.023, 0.023) 11.445 (11.424, 11.466)
Flux (units?), Zeiss Commercial 119 0.311 0.011 (0.011, 0.011) 0.031 (0.030, 0.031) 3.540 (3.532, 3.548)

Calculating Repeatability Statistics

Explanations of repeatability statistic calculations

Within-Subject Mean \((\mu_w)\)

\(\mu_w\) is the average of all measurements of one eye for a given individual. The overall mean \((\mu)\) is calculated by taking the mean of \(\mu_w\) across the dataset. The overall mean is included in the final table for reference.

\[ \mu_w = \frac{1}{M}\sum_{i=1}^{M} x_i \]

\[\text{where } M \text{ is the number of measurements per eye,}\]

Within-Subject Standard Deviation \((S_w)\)

Find \(S_w\) by first calculating the variance of the measurements per individual eye. The equation below is general for any number of measurements; in this study there are at least 2 measurements per eye, but sometimes more.

\[ \sigma^2_{measurement} = \frac{1}{M}\sum_{i=1}^{M} (x_i - \mu_w)^2 \]

\[ \text{where } M \text{ is the number of measurements per eye} \]

To calculate \(S_w\), average of the variance of measurements \((\sigma^2_{measurement})\) for all eyes measured, then take the square root.

\[ Sw = \sqrt{\frac{1}{N}\sum_{i=1}^{N}\sigma^2_{measurement,i}} \]

\[ \text{where } N \text{ is the number of eyes measured} \]

Within-Subject Coefficient of Repeatability \((CR_w)\)

The \(CR_w\) provides the uncertainty of repeated measures.

\[ CRw = \sqrt2 * 1.96 * Sw \]

The \(CR_w\) can be interpreted as:

“The difference between two measurements for the same subject is expected to be less than [\(CR_w\)] for 95% of pairs of observations.”3

Within-Subject Coefficient of Variation \((CV_w)\)

\[ CVw = 100 *\frac{Sw}{\mu} \]

Intraclass Correlation Coefficient, Unadjusted

Intraclass Correlation Coefficient (ICC) is scored using the ICCest() function from the ICC package. This function “estimates the ICC and confidence intervals using the variance components from a one-way ANOVA.”

This is a preliminary result, as we want to calculate the ICC after adjusting for participant, eye (left or right), signal strength, and clinical and other variables. This will be done later in the mixed effects regression models.

Intra-Visit ICC, Unadjusted

Normal

OCTA Variable n_people ICC ICC 95% CL k varw vara
Vessel Diameter (units?) 68 0.669 (0.546, 0.771) 2.646 0.185 0.373
Vessel Area Density (units?) 68 0.785 (0.694, 0.855) 2.646 0.000 0.001
Vessel Area Density (units?), Zeiss Commercial 68 0.935 (0.902, 0.957) 2.646 0.000 0.000
Vessel Skeleton Density (units?) 68 0.786 (0.696, 0.856) 2.646 0.000 0.000
Vessel Perimeter Index (units?) 68 0.779 (0.687, 0.851) 2.646 0.000 0.001
Vessel Complexity Index (units?) 68 0.774 (0.680, 0.847) 2.646 210266.849 721358.797
Flow Impairment Zone (units?) 68 0.729 (0.621, 0.815) 2.646 3.304 8.873
Flux (units?) 68 0.805 (0.721, 0.869) 2.646 0.000 0.000
Flux (units?), Zeiss Commercial 68 0.930 (0.896, 0.954) 2.646 0.000 0.001

Glaucoma

OCTA Variable n_people ICC ICC 95% CL k varw vara
Vessel Diameter (units?) 81 0.909 (0.869, 0.939) 2.54 0.235 2.349
Vessel Area Density (units?) 81 0.912 (0.873, 0.940) 2.54 0.000 0.004
Vessel Area Density (units?), Zeiss Commercial 81 0.972 (0.959, 0.981) 2.54 0.000 0.002
Vessel Skeleton Density (units?) 81 0.915 (0.877, 0.942) 2.54 0.000 0.001
Vessel Perimeter Index (units?) 81 0.911 (0.872, 0.940) 2.54 0.000 0.003
Vessel Complexity Index (units?) 81 0.911 (0.871, 0.940) 2.54 223612.517 2280565.529
Flow Impairment Zone (units?) 81 0.883 (0.833, 0.920) 2.54 3.592 27.057
Flux (units?) 81 0.923 (0.888, 0.948) 2.54 0.000 0.001
Flux (units?), Zeiss Commercial 81 0.966 (0.950, 0.977) 2.54 0.000 0.001

Inter-Visit ICC, Unadjusted

Inter-Visit ICC Normal

Normal, All

OCTA Variable n_people ICC ICC 95% CL k varw vara
Vessel Diameter (units?) 67 0.518 (0.343, 0.664) 2.251 0.321 0.345
Vessel Area Density (units?) 67 0.751 (0.637, 0.835) 2.251 0.001 0.002
Vessel Area Density (units?), Zeiss Commercial 67 0.842 (0.763, 0.897) 2.251 0.000 0.000
Vessel Skeleton Density (units?) 67 0.736 (0.617, 0.825) 2.251 0.000 0.000
Vessel Perimeter Index (units?) 67 0.743 (0.626, 0.829) 2.251 0.000 0.001
Vessel Complexity Index (units?) 67 0.734 (0.614, 0.823) 2.251 320437.325 884489.617
Flow Impairment Zone (units?) 67 0.692 (0.558, 0.793) 2.251 5.013 11.239
Flux (units?) 67 0.655 (0.511, 0.767) 2.251 0.000 0.000
Flux (units?), Zeiss Commercial 67 0.832 (0.749, 0.891) 2.251 0.000 0.001

Normal, 365 Days

OCTA Variable n_people ICC ICC 95% CL k varw vara
Vessel Diameter (units?) 40 0.461 (0.201, 0.667) 2.122 0.478 0.410
Vessel Area Density (units?) 40 0.704 (0.519, 0.828) 2.122 0.001 0.002
Vessel Area Density (units?), Zeiss Commercial 40 0.871 (0.776, 0.928) 2.122 0.000 0.000
Vessel Skeleton Density (units?) 40 0.695 (0.506, 0.823) 2.122 0.000 0.000
Vessel Perimeter Index (units?) 40 0.693 (0.504, 0.822) 2.122 0.001 0.001
Vessel Complexity Index (units?) 40 0.683 (0.489, 0.815) 2.122 434047.038 933825.269
Flow Impairment Zone (units?) 40 0.665 (0.464, 0.804) 2.122 6.352 12.586
Flux (units?) 40 0.728 (0.554, 0.843) 2.122 0.000 0.000
Flux (units?), Zeiss Commercial 40 0.877 (0.786, 0.932) 2.122 0.000 0.001

Normal, 180 Days

OCTA Variable n_people ICC ICC 95% CL k varw vara
Vessel Diameter (units?) 19 0.266 (-0.128, 0.616) 2.198 0.795 0.288
Vessel Area Density (units?) 19 0.559 (0.209, 0.795) 2.198 0.001 0.001
Vessel Area Density (units?), Zeiss Commercial 19 0.807 (0.598, 0.918) 2.198 0.000 0.000
Vessel Skeleton Density (units?) 19 0.545 (0.190, 0.787) 2.198 0.000 0.000
Vessel Perimeter Index (units?) 19 0.537 (0.180, 0.783) 2.198 0.001 0.001
Vessel Complexity Index (units?) 19 0.516 (0.153, 0.771) 2.198 639206.657 681654.525
Flow Impairment Zone (units?) 19 0.521 (0.159, 0.774) 2.198 9.792 10.630
Flux (units?) 19 0.539 (0.182, 0.784) 2.198 0.000 0.000
Flux (units?), Zeiss Commercial 19 0.699 (0.413, 0.867) 2.198 0.000 0.000

Inter-Visit ICC Glaucoma

Glaucoma

OCTA Variable n_people ICC ICC 95% CL k varw vara
Vessel Diameter (units?) 81 0.882 (0.835, 0.919) 2.881 0.351 2.632
Vessel Area Density (units?) 81 0.728 (0.634, 0.805) 2.881 0.001 0.003
Vessel Area Density (units?), Zeiss Commercial 81 0.958 (0.939, 0.971) 2.881 0.000 0.002
Vessel Skeleton Density (units?) 81 0.753 (0.666, 0.825) 2.881 0.000 0.001
Vessel Perimeter Index (units?) 81 0.749 (0.661, 0.822) 2.881 0.001 0.003
Vessel Complexity Index (units?) 81 0.767 (0.684, 0.835) 2.881 621776.618 2048184.010
Flow Impairment Zone (units?) 81 0.705 (0.606, 0.788) 2.881 9.571 22.904
Flux (units?) 81 0.724 (0.630, 0.803) 2.881 0.000 0.000
Flux (units?), Zeiss Commercial 81 0.876 (0.826, 0.914) 2.881 0.000 0.001

Glaucoma, 365 Days

OCTA Variable n_people ICC ICC 95% CL k varw vara
Vessel Diameter (units?) 62 0.893 (0.840, 0.931) 2.704 0.354 2.947
Vessel Area Density (units?) 62 0.746 (0.639, 0.830) 2.704 0.001 0.004
Vessel Area Density (units?), Zeiss Commercial 62 0.958 (0.937, 0.973) 2.704 0.000 0.002
Vessel Skeleton Density (units?) 62 0.777 (0.681, 0.852) 2.704 0.000 0.001
Vessel Perimeter Index (units?) 62 0.768 (0.668, 0.845) 2.704 0.001 0.003
Vessel Complexity Index (units?) 62 0.786 (0.692, 0.858) 2.704 599810.232 2200298.471
Flow Impairment Zone (units?) 62 0.720 (0.605, 0.811) 2.704 9.303 23.878
Flux (units?) 62 0.747 (0.641, 0.831) 2.704 0.000 0.000
Flux (units?), Zeiss Commercial 62 0.886 (0.831, 0.926) 2.704 0.000 0.001

Glaucoma, 180 Days

OCTA Variable n_people ICC ICC 95% CL k varw vara
Vessel Diameter (units?) 48 0.931 (0.889, 0.959) 2.47 0.245 3.326
Vessel Area Density (units?) 48 0.879 (0.808, 0.928) 2.47 0.001 0.004
Vessel Area Density (units?), Zeiss Commercial 48 0.954 (0.924, 0.973) 2.47 0.000 0.002
Vessel Skeleton Density (units?) 48 0.899 (0.837, 0.939) 2.47 0.000 0.001
Vessel Perimeter Index (units?) 48 0.886 (0.818, 0.932) 2.47 0.000 0.004
Vessel Complexity Index (units?) 48 0.891 (0.826, 0.935) 2.47 303585.484 2489439.769
Flow Impairment Zone (units?) 48 0.796 (0.684, 0.875) 2.47 6.957 27.072
Flux (units?) 48 0.883 (0.813, 0.930) 2.47 0.000 0.001
Flux (units?), Zeiss Commercial 48 0.911 (0.857, 0.947) 2.47 0.000 0.001

Calculating ICC Statistic

\[ \text{ICC} = \frac{\text{between}}{\text{between} + \text{within}}\]

“In the output for the random effects model ‘SID’ is the estimated between-group variance, which in the ICCest output is called ‘vara’ (variance among groups). The within-group variance is ‘Residual’ in the random effects model output, while in ICCest it’s called ‘varw.’ You can see that the values for those two variances match perfectly in the two different outputs. The ICC is defined as between/(between+within). That calculation is not part of the random effects model output, but it is part of the ICCest output, along with confidence intervals for the ICC estimate. The ICC are really high for intravisit (around 97%) and a little lower for intervisit (about 94%). If we were to calculate these ICC for glaucoma and controls separately I think they would be significantly lower because of the reduced between-group variability.” - BB 9/4/2019

ARVO Abstract Tables

Table 1: Participants

Overall there were:

  • 332 measurements of 68 patients without glaucoma

  • 462 measurements of 81 patients with glaucoma

Among intravisit data there were:

  • 180 measurements of 68 patients without glaucoma

  • 206 measurements of 81 patients with glaucoma

Among intervisit data there were:

  • 151 measurements of 67 patients without glaucoma

  • 235 measurements of 81 patients with glaucoma

None Glaucoma p test
n 68 82
Sociodemographic Variables
age (mean (SD)) 50.74 (16.26) 61.78 (14.50) <0.001
Sex = Male (%) 33 (48.5) 39 ( 47.6) 1.000
Systemic Clinical Variables
Hypertension Diagnosis = Yes (%) 15 (22.1) 28 ( 34.1) 0.148
Diabetes Mellitus Diagnosis = Yes (%) 3 ( 4.4) 14 ( 17.1) 0.030
Optic Neuropathy = Yes (%) 1 ( 1.5) 0 ( 0.0) 0.925
Ophthalmic Clinical Variables
Glaucoma Diagnosis, Binary = Glaucoma (%) 0 ( 0.0) 82 (100.0) <0.001
Diabetic Retinopathy Diagnosis, Binary = Yes (%) 0 ( 0.0) 4 ( 4.9) 0.181
Ophthalmic Surgical Variables
Surgical Procedure for Cataract Extraction = Yes (%) 8 (11.8) 21 ( 25.6) 0.054
Surgical Procedure for Glaucoma (%) <0.001
None 62 (91.2) 45 ( 54.9)
Laser 6 ( 8.8) 18 ( 22.0)
Minimally Invasive Glaucoma Surgery 0 ( 0.0) 1 ( 1.2)
Filter 0 ( 0.0) 18 ( 22.0)
OCT Angiography Signal Strength
signal_strength (mean (SD)) 9.50 (0.64) 9.16 (0.79) 0.005

Table 2: Repeatability Statistics

OCTA Variable
Mean
ICC
Sw
CRw
CVw
None
Glaucoma
None
Glaucoma
None
Glaucoma
None
Glaucoma
None
Glaucoma
var_name_normal µ_normal µ_glc ICC_pretty_normal ICC_pretty_cl_normal ICC_pretty_glc ICC_pretty_cl_glc Sw_pretty_normal Sw_pretty_cl_normal Sw_pretty_glc Sw_pretty_cl_glc CRw_pretty_normal CRw_pretty_cl_normal CRw_pretty_glc CRw_pretty_cl_glc CVw_pretty_normal CVw_pretty_cl_normal CVw_pretty_glc CVw_pretty_cl_glc
Vessel Area Density (units?) 0.359 0.281 0.785 (0.694, 0.855) 0.912 (0.873, 0.940) 0.021 (0.021, 0.021) 0.019 (0.019, 0.019) 0.059 (0.058, 0.059) 0.052 (0.051, 0.052) 5.884 (5.800, 5.967) 6.642 (6.609, 6.674)
Vessel Area Density (units?), Zeiss Commercial 0.429 0.398 0.935 (0.902, 0.957) 0.972 (0.959, 0.981) 0.006 (0.006, 0.006) 0.007 (0.007, 0.007) 0.016 (0.016, 0.016) 0.019 (0.019, 0.019) 1.369 (1.368, 1.371) 1.748 (1.746, 1.751)
Vessel Skeleton Density (units?) 0.139 0.105 0.786 (0.696, 0.856) 0.915 (0.877, 0.942) 0.009 (0.009, 0.009) 0.008 (0.008, 0.008) 0.026 (0.026, 0.026) 0.023 (0.022, 0.023) 6.716 (6.672, 6.760) 7.751 (7.734, 7.767)
Flux (units?) 0.108 0.079 0.805 (0.721, 0.869) 0.923 (0.888, 0.948) 0.008 (0.008, 0.008) 0.007 (0.007, 0.007) 0.022 (0.022, 0.023) 0.019 (0.019, 0.019) 7.485 (7.451, 7.520) 8.479 (8.465, 8.492)
Flux (units?), Zeiss Commercial 0.360 0.320 0.930 (0.896, 0.954) 0.966 (0.950, 0.977) 0.007 (0.007, 0.007) 0.007 (0.007, 0.007) 0.018 (0.018, 0.018) 0.019 (0.019, 0.019) 1.847 (1.844, 1.849) 2.098 (2.095, 2.101)

Mixed Effects Regression Models

Model Fitting

“For the markdown file let’s just spit out all the output from the random effects model and the iccest command so we can show it to Grace. Eventually we can put the ICC in the table with the other repeatability measures you have already tabled but I don’t think we need it for the meeting.” - BB 9/4/2019

## Linear mixed model fit by REML ['lmerMod']
## Formula: v_area_density ~ (1 | ptid)
##    Data: data_octa_global_intra
## 
## REML criterion at convergence: -1418.6
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -4.8944 -0.3556  0.0261  0.3420  4.6712 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  ptid     (Intercept) 0.004471 0.06687 
##  Residual             0.000393 0.01983 
## Number of obs: 386, groups:  ptid, 149
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept) 0.314779   0.005575   56.47

“I also added a model to test whether SS influences reliability. The reference level is ‘10’ now, which is what we want, and you can see that SS is highly associated with VAD, meaning it affects reliability.” - BB 9/4/2019

## Linear mixed model fit by REML ['lmerMod']
## Formula: v_area_density ~ signal_strength + (1 | ptid)
##    Data: data_octa_global_intra
## 
## REML criterion at convergence: -1425.8
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -4.9013 -0.3343  0.0233  0.3362  4.6693 
## 
## Random effects:
##  Groups   Name        Variance  Std.Dev.
##  ptid     (Intercept) 0.0039954 0.06321 
##  Residual             0.0003926 0.01982 
## Number of obs: 386, groups:  ptid, 149
## 
## Fixed effects:
##                 Estimate Std. Error t value
## (Intercept)     0.210636   0.024986   8.430
## signal_strength 0.011185   0.002622   4.265
## 
## Correlation of Fixed Effects:
##             (Intr)
## sgnl_strngt -0.977

References

1. Venugopal JP, Rao HL, Weinreb RN, et al. Repeatability and comparability of peripapillary vessel density measurements of high-density and non-high-density optical coherence tomography angiography scans in normal and glaucoma eyes. The British Journal of Ophthalmology 2019;103:949–954.

2. Venugopal JP, Rao HL, Weinreb RN, et al. Repeatability of vessel density measurements of optical coherence tomography angiography in normal and glaucoma eyes. The British Journal of Ophthalmology 2018;102:352–357.

3. Bland JM, Altman DG. Statistics Notes: Measurement error. BMJ : British Medical Journal 1996;313:744.